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- PDB-2jcd: Structure of the N-oxygenase AurF from Streptomyces thioluteus -

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Basic information

Entry
Database: PDB / ID: 2jcd
TitleStructure of the N-oxygenase AurF from Streptomyces thioluteus
ComponentsN-OXIDASE
KeywordsOXIDOREDUCTASE / OXIDATION OF P-BENZOIC ACID / N-OXYGENASE / DI-MANGANESE MONO-OXYGENASE
Function / homology
Function and homology information


4-aminobenzoate N-oxygenase / oxidoreductase activity / metal ion binding / identical protein binding
Similarity search - Function
: / P-aminobenzoate N-oxygenase AurF / P-aminobenzoate N-oxygenase AurF / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / 4-aminobenzoate N-oxygenase
Similarity search - Component
Biological speciesSTREPTOMYCES THIOLUTEUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
AuthorsZocher, G.E. / Winkler, R. / Hertweck, C. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Action of the N-Oxygenase Aurf from Streptomyces Thioluteus.
Authors: Zocher, G.E. / Winkler, R. / Hertweck, C. / Schulz, G.E.
History
DepositionDec 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-OXIDASE
B: N-OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,84513
Polymers78,1912
Non-polymers65411
Water7,873437
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-44.2 kcal/mol
Surface area32610 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.222, 115.438, 125.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.290222, -0.044259, 0.955935), (-0.057699, -0.996303, -0.063645), (0.955218, -0.073628, 0.286595)
Vector: 21.9659, 81.792, -11.6058)

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Components

#1: Protein N-OXIDASE / N-OXYGENASE AURF


Mass: 39095.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES THIOLUTEUS (bacteria) / Plasmid: PMAL-C2X/AURF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70KH9
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.90806
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90806 Å / Relative weight: 1
ReflectionResolution: 2.11→62 Å / Num. obs: 52924 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
XDSdata reduction
SHELXphasing
SHARPphasing
PHASERphasing
ARP/wARPphasing
REFMACphasing
Cootphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.11→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.414 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2645 5 %RANDOM
Rwork0.196 ---
obs0.198 50255 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--0.86 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.11→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4975 0 32 437 5444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.967181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5922.5256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19915897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481567
X-RAY DIFFRACTIONr_chiral_restr0.1010.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024065
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.22853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23695
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.53364
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61825243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28132199
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5594.51936
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.17 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 193
Rwork0.221 3661

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